Peer Review History
| Original SubmissionMay 31, 2020 |
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PONE-D-20-16432 Analysis of the time and age dependence of the case-fatality-ratio for COVID-19 in seven countries with a high total-to-positive test ratio suggests that the true CFR may be significantly underestimated for the United States in current models PLOS ONE Dear Dr. Rothman, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. Please ensure that your decision is justified on PLOS ONE’s publication criteria and not, for example, on novelty or perceived impact. ============================== Please submit your revised manuscript by Oct 18 2020 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. Please include the following items when submitting your revised manuscript:
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The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and 2. We note that you have indicated that data from this study are available upon request. PLOS only allows data to be available upon request if there are legal or ethical restrictions on sharing data publicly. For information on unacceptable data access restrictions, please see http://journals.plos.org/plosone/s/data-availability#loc-unacceptable-data-access-restrictions. In your revised cover letter, please address the following prompts: a) If there are ethical or legal restrictions on sharing a de-identified data set, please explain them in detail (e.g., data contain potentially identifying or sensitive patient information) and who has imposed them (e.g., an ethics committee). Please also provide contact information for a data access committee, ethics committee, or other institutional body to which data requests may be sent. b) If there are no restrictions, please upload the minimal anonymized data set necessary to replicate your study findings as either Supporting Information files or to a stable, public repository and provide us with the relevant URLs, DOIs, or accession numbers. Please see http://www.bmj.com/content/340/bmj.c181.long for guidelines on how to de-identify and prepare clinical data for publication. For a list of acceptable repositories, please see http://journals.plos.org/plosone/s/data-availability#loc-recommended-repositories. We will update your Data Availability statement on your behalf to reflect the information you provide. 3. Thank you for stating the following financial disclosure: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." At this time, please address the following queries: a) Please clarify the sources of funding (financial or material support) for your study. List the grants or organizations that supported your study, including funding received from your institution. b) State what role the funders took in the study. If the funders had no role in your study, please state: “The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.” c) If any authors received a salary from any of your funders, please state which authors and which funders. d) If you did not receive any funding for this study, please state: “The authors received no specific funding for this work.” Please include your amended statements within your cover letter; we will change the online submission form on your behalf 4. Please include your tables as part of your main manuscript and remove the individual files. Please note that supplementary tables (should remain/ be uploaded) as separate "supporting information" files 5. Please include captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Yes Reviewer #2: Partly ********** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: No Reviewer #2: No ********** 3. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: No Reviewer #2: Yes ********** 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: No Reviewer #2: Yes ********** 5. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: I suggest readers shortening the title and let readers quickly catch the whole concept and purpose of this study at a quick glance. The number of Tables and Figures should be condensed to report the main findings in this study. Figure 6 is nice but the computation of ture CFR should be easy to follow for non-specialist Reviewer #2: Summary: The authors study age and time dependence of the case fatality ratio in a handful of example countries. The questions asked by the authors are certainly important. The data is presented in a useful way and many of the conclusions reached are consistent with the best available evidence for different severity estimates of COVID. However, I believe the paper has a number of methodological and presentational shortcomings. I believe the paper is not of publishable standard currently and to be frank it would need almost a complete overhaul before it would be publishable. Major comments: Most of the mathematics in the text I believe needs to be re-written and re-formatted for readability, as it is currently, its incredibly hard to read as it doesn't flow. It includes many uses of plain english ("CFR", age ranges, "corrected" etc), which make it almost impossible to read. On top of that, the logic that the authors are trying to move through as they describe the methods often feels clunky. Its not completely clear why certain choices are made for example. The methods include some overstated claims I believe. For example, the subsection called "Optimization of the parameters of f_D" I do not believe is describing parameter optimisation. I could be wrong, but based on how it is currently written, it seems as though a couple of arbitrary choices were made for medians and log SDs of the distribution and inspecting the goodness of fit. So perhaps the optimal parameters out of the three or so choices of median were determined, but the section is misleading. Why were these choices made. To be frank, I believe this style of modelling is of quite poor standard I am very surprised that there is no mention of under-ascertainment of cases as a source of bias when estimating the CFR of COVID. It is well-known that many, even most in some countries, of symptomatic cases are (or at least have been, during peaks of certain countries epidemics) under-ascertained. This can bias estimates of the CFR, along with many other important epidemiological quantities upwards significantly. The authors must mention this at the very least. If the purpose of the paper is to provide accurate CFR estimates, the authors need to adjust for this. I don't see any attempt to do this in the current form of the manuscript. The methods are often very crude. For example, dividing by 2 to move from CFR to IFR, because roughly half of the infections were asymptomatic on the Diamond Princess. The proportion of symotomatic/asymptomatic on the Diamond Princess is known and publicly available, so using the exact ratio is very easy. Furthermore, accurate inferred estimates of this proportion and its dependency on age have been estimated, using very detailed transmission models and fitted using MCMC. I can't quite understand why accurate estimates have not been used and very crude unjustified methods have been used. There is somewhat of a mismatch between the detail in descriptive data and some of the estimates and the crudeness of some elements of the methods. The authors are clearly aware that accuracy is required when reporting important estimates. However, they seem far less aware that the same level of accuracy and rigor is required in the methods, especially when more accurate/rigorous approaches are not much more effort or difficult (given the inordinate of high quality studies on COVID already available). ********** 6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: No Reviewer #2: No [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. 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| Revision 1 |
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PONE-D-20-16432R1 Analysis of the time course of COVID-19 cases and deaths from countries with extensive testing allows accurate early estimates of the age specific symptomatic CFR values PLOS ONE Dear Dr. Rothman, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. Please submit your revised manuscript by Feb 22 2021 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. Please include the following items when submitting your revised manuscript:
If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter. If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols We look forward to receiving your revised manuscript. Kind regards, Wenbin Tan Academic Editor PLOS ONE In summary, this article is of importance in particular comparison of CFR and IFR made among countries during the COVID-19 epidemic. For improving the readability of this article, several questions should be classified further before consideration of publication in the journal of PLOS ONE. Major concerns: 1. It is hard to read this article for reviewers when no double spaces remained between lines. 2. Why manuscript cannot be as abstract with the formal structure of Background(or Introduction in context), Methods, Results, and Discussion(or plus condition in context). The Sources of data after Introduction is weird and rare in the format of formal scientific articles. 3. In line 3 in the Introduction, (referred to as the case fatality ratio, CFR) and infected cases (IFR) instead of infected fatality rate(IFR) used in this study. 4. At the first time to report the terms such as IFT and CFR that should be defined clearly as those in WIKI at https://en.wikipedia.org/wiki/Case_fatality_rate 5. In the Introduction, we have not been aware of the reason for conducting this study and the purpose of this study. Using Table 1 in the Introduction is rare in the scientific article. How to make a concise introduction for readers to capture the motivation and purpose of this study is of importance. For instance, using the correct CFRs with each other in countries is essential and necessary. 6. It is important for readers who are able to replicate a similar study in the future. We have not seen any that could help readers redo the study in future studies. Although authors addressed that the dataset can be provided after acceptance in the publication in response to the reviewer’s comments, the focus is not on the total fully dataset, but the calculation or process of the model parameter estimation that readers hope to understand even a partial or piece of data is enough. In this revised manuscript, I have also not been aware of any about the correct CFR calculation that can be understandable for readers. 7. In Sources of data, the definitions of symbols in equations should be followed after the formula or equation. For instance, the symbol of I for Infection: individuals who are symptomatic or asymptomatic has not found any in the formula. Keep in mind, authors should make efforts to let readers replicate and understand the study completely. Otherwise, all study are in vein. Similarly, the structure of manuscript that should be in accordance with the common style and format is necessary to be similar to (or at least not different from) other’s thinking process. For example, the section on Optimization of the parameters of fD should let us know how to obtain the fD rather than using the narrative only in the paragraph, but describing what software or statistics used in this study. That is, we are interested in this part of the study because it is important in epidemiology. An example that can be illustrated in this study is wonderful to make readers easy capture the core of this study. It is a pity to waste the efforts made by the authors in this study because the calculation or parameter estimation is not clear and not understandable. Any result or discussion in Results and Discussion to explain the reason for the gap and difference in real-world is unnecessary. 8. I appreciate this study topic that is of interest and importance. Hopefully, this major concern can be improved in the next run of manuscript submission. Minor concerns: Grammar to be improved In Abstract: age dependent CFR time courses to explain this increase and to - age-dependent CFT…….. Age dependent time to fatality corrected CFR was calculated using two independent - age-dependent time to fatality…….. A linear model was developed that predicts CFR based on age dependent CFR -age-dependent CFR…….. coefficients and the age distribution of cases. The model was tested by a linear regression of each country’s CFR against case percentage of 70 years and over. - by linear regression The linear model based on their age specific CFR values provides an alternative - age-specific CFR Introduction: For the United States and United Kingdom, even lower true CFR and IFR values have been reported --- the United Kingdom reexamined the reported number of fatalities and nCFR values outbreaks on May 7, 2020 for -2020, for Australia, Austria, Germany, Iceland, Israel, New Zealand, and South Korea. In all cases these countries continued to have a high degree of testing and tracking and testing of contacts as - In all cases, these…… United States and 8:1 for the United Kingdom, (Appendix 4). Therefore, their final reported - the United Kingdom (Appendix 4) CFR values even early in the outbreaks when the reported nCFR values were several fold lower. -several folds lower for the United States and United Kingdom.(5,10,13,14) Despite this range, the large - the United Kingdom From this model we estimated the corrected CFR for China using the linear model from the case - From this model, in total number of fatalities recently reported by the Chinese government.(2) Regarding US and UK populations, there is a much wider range of CFR and IFR estimates, with -- A total number of ……. We therefore tested our model by calculating the percent of the population who has been -, therefore, onset (day of positive test) to fatality distributions for Chinese patients outside of Wuhan who A positive test censoring (fatalities missed due to the limited patient observation time). The best fitting distributions from these sources were very similar, with Linton reporting a best fit median of - best-fitting 13.2 days with a 95% CI of 11.5 to 15.3 days, and Mizumoto et al. reporting a best fit median - the best fit median all studies, based on gamma fits, was very similar, and equivalent to a logSD of approximately --- very similar and equivalent Goodness of fit was then determined by calculating the least squares total residual - The goodness of fit was…. the population and the age specific CFR values. Studies have reported that the nCFR - age-specific DFR COVID-19 strongly increases with age.(5–7,9–11,15,21,22,32–34) We determined for country the corrected CFR values for the fraction of a country’s populations of age - for a fraction - cumulative fatalities (Appendix 5). Case per day data from South Korea and Germany - per day of data from….. shifted several days later and a less right skewed distribution.(1,5,32) Based on these - right-skewed distribution population infected, we then divided the maximum and minimum number of - and a minimum number of due to the random testing not including children, who are known to have a much – - , not including children, plot using the South Korean data, which rose from a low of 0.55% on March 8, 2020 to its value -2020, on May 7, 2020 of 2.28%. The values shown are plotted from 10 days after the first 2020, were reported to avoid large fluctuations, these due to the low number of fatalities - fluctuations due to the low number of Figure 1. Reported nCFR(t) increases with time after outbreak for Germany. The nCFR the outbreak for Germany continuously increased with time after the outbreak, from a lowest value of 0.12% on March 10, 2020 to -2020, its present value on May 7, 2020 of 4.36%. The dashed horizontal line at 5.0% is our -2020, CFR from the closed case CFR value. Figure 2. Reported nCFR(t) versus day after outbreak for South Korea. The nCFR for South Korea is also seen to be continuously increasing from a minimum of 0.55% on March 8, 2020 to 2.28% -2020, curve, the closed case fatality ratio appears to be converging to a near constant value. In contrast the a near-constant mean of 0.129- 0.204, which is within error the same as the slope determined by linear regression value. -the liear regression value cCFR70+ + cCFR69. It is seen that for all countries the cCFR70 term explains the large - for all countries, the New York City population that has been infected by COVID-19 up through April 22, 2020 in order to compare with recent studies that have performed random -0 -2020, College model, the estimated percentages of the population infected are several fold above the -several-fold corrections for missed cases.(3–11,20–22,34) We found that in all cases there was a several fold increase in -that in all cases, several-fold n between diagnosis and fatality. Despite the high level of testing we found a wide --- -f testing, When we examined the component of the CFR due to this population (cCFR70+) --- -componence of April 22, 2020 was 2 to 16.5-fold higher than previous values that have been applied -2020, between 70 and 79 and 80 and over years old, but higher than the majority but not - over the years old least several fold from the early values used to justify low estimates of the IFR for COVID-19 -several-fold (see Figures 5A, 5B, and Appendix 3).(12,14,24–27,30) We therefore calculated the -, therefore, We did not factor in preexisting conditions in our analysis which has been reported - missing verb???? fraction of the case population in the 60 – 69 group which also has a highly elevated -, which also has a highly 27) However due to the low number of fatalities in several countries in the 0- 69 age -. However, did not perform a sub analysis. -sub-analysis. asymptomatic. This value may be an overestimate, as shown by Mizumoto, because - by Mizumote because….. possibility in which none of the active cases as of April 22, 2020 subsequently died --- -2020, COVID-19 (33 out of 215 having the virus).(16) In the second study the New York City -in the second study, of time, and corrected for age distribution of positive cases.(11) No time correction - for the age distribution |
| Revision 2 |
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PONE-D-20-16432R2 Analysis of the time course of COVID-19 cases and deaths from countries with extensive testing allows accurate early estimates of the age specific symptomatic CFR values PLOS ONE Dear Dr. Rothman, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. Please submit your revised manuscript by Jun 03 2021 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. Please include the following items when submitting your revised manuscript:
If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter. If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols. We look forward to receiving your revised manuscript. Kind regards, Wenbin Tan Academic Editor PLOS ONE Reviewers' comments: Reviewer #4: This study provides an important method to predict COVID-19 infection by calculating age specific symptomatic CFR values. However, the whole article is not well organized to show the significant finding: 1. The introduction in current status need to revised to illustrate the importance, necessity and motivation of estimates of the age specific symptomatic CFR values. Also, using table in the introduction is not a common practice for scientific papers. Please move it to result or supplementary section. 2. The procedures 1-6 is more like methods, please simplify this part and introduce the most important information or findings. 3. It’s easier for reader to detail the statistics method and software used in this study, instead of using mathematical formula. For example, what kind of regression were used to validate age dependent CFRcrudetimecorrected values. 4. The figure and table should use canonical standards for scientific articles. For example, There is no necessary to mark each day in the horizontal axis in figure 1 and 2. ********** |
| Revision 3 |
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Analysis of the time course of COVID-19 cases and deaths from countries with extensive testing allows accurate early estimates of the age specific symptomatic CFR values PONE-D-20-16432R3 Dear Dr. Rothman, We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements. Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication. An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org. If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. Kind regards, Wenbin Tan Academic Editor PLOS ONE |
| Formally Accepted |
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PONE-D-20-16432R3 Analysis of the time course of COVID-19 cases and deaths from countries with extensive testing allows accurate early estimates of the age specific symptomatic CFR values Dear Dr. Rothman: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact onepress@plos.org. If we can help with anything else, please email us at plosone@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Wenbin Tan Academic Editor PLOS ONE |
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